When Microsoft acquired Yammer, the original plan unveiled by Yammer founder and CEO David Sacks and Microsoft CEO Steve Ballmer was to keep Yammer intact, with everyone in the company reporting to Sacks.

Already, the marketing department reports up to a Microsoft executive, out of Sacks's chain of command. In a few months, the same will be true of sales.

It appears that most Yammer salespeople will become product specialists—sometimes called "black belts"—working alongside Microsoft account managers.

Salespeople already know about the pending move, as they seek new jobs within Microsoft's sales force, but Yammer's management has not informed the rest of the company about the plan.

That lack of transparency, more than the layoffs, has employees particularly upset, we're hearing. As a startup, Yammer practiced an open culture, where company matters were shared and discussed widely—typically using Yammer's own software.

Yammer also holds periodic all-hands meetings known as Yammer Time. We understand that Sacks addressed the recent layoffs but did not mention the upcoming changes in the sales operation at today's meeting.

The change in the marketing department was pushed by Yammer executives. It's not clear whether Microsoft or Yammer executives prompted the handover of sales to Microsoft.

Integrating with Microsoft seems sensible, even inevitable. Sacks has made references to taking advantage of Microsoft's sales force in previous interviews. But the pace of change and the way it's being communicated are raising questions about how Microsoft and Yammer are handling the company's integration.

How Microsoft handles Yammer is a question of intense interest outside the company as well as inside. If Microsoft is seen as rushing the integration or mistreating employees, it may make other startups reluctant to sell to Microsoft.